Able to speak Albanian very well, he came to Albania in the early 1990s after the fall of the atheist government of Albania where he joined in the restoration of the Orthodox church in Albania. For twenty years he served the Metropolis of Gjirokastra in southern Albania, preached the word of God among its remote villages, baptizing and serving the Holy Mysteries. His evangelization earned him the deep respect of believers and of those who came to know him. During these years he was raised to the dignity of archimandrite.

On January 19, 2012, Archim. Nathaniel was elected Bishop of Amantia by the Holy Synod of the Church of Albania.